Trapping/Pinning of colloidal microspheres over glass substrate using surface features

Suspensions of micro and nano particles made of Polystyrene, Poly(methyl methacrylate), Silicon dioxide etc. have been a standard model system to understand colloidal physics. . These systems have proved useful insights into phenomena such as self-assembly. Colloidal model systems are also extensively used to simulate many condensed matter phenomena such as dynamics in a quenched disordered system and glass transition. A precise control of particles using optical or holographic tweezers is essential for such studies. However, studies of collective phenomena such as jamming and flocking behaviour in a disordered space are limited due to the low throughput of the optical trapping techniques.In this article, we present a technique where we trap and pin polystyrene microspheres ~ 10 {\mu}m over triangular-crest shaped microstructures in a microfluidic environment. Trapping/Pinning occurs due to the combined effect of hydrodynamic interaction and non-specific adhesion forces. This method allows trapping and pinning of microspheres in any arbitrary pattern with a high degree of spatial accuracy which can be useful in studying fundamentals of various collective phenomena as well as in applications such as bead detachment assay based biosensors

Detection Limit for Optically Sensing Specific Protein Interactions in Free-solution

Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index change arising from protein-protein interactions. The model, based on the Maxwell Garnett effective medium theory and first order chemical kinetics serves as a general framework for estimating the detection limits of optical sensing of molecular interactions. The model is applicable to situations where one interacting species is immobilized to a surface, as commonly done, or to emerging techniques such as Back-Scattering Interferometry (BSI) where both interacting species are un-tethered. Our findings from this model point to the strong role of as yet unidentified factors in the origin of the BSI signal resulting in significant deviation from linear optical response.Comment: 7 Page Manuscript + 14 Page Supplementary Informatio

Tuning the torque-speed characteristics of bacterial flagellar motor to enhance the swimming speed

In a classic paper, Edward Purcell analysed the dynamics of flagellated bacterial swimmers and derived a geometrical relationship which optimizes the propulsion efficiency. Experimental measurements for wild-type bacterial species E. coli have revealed that they closely satisfy this geometric optimality. However, the dependence of the flagellar motor speed on the load and more generally the role of the torque-speed characteristics of the flagellar motor is not considered in Purcell's original analysis. Here we derive a tuned condition representing a match between the flagella geometry and the torque-speed characteristics of the flagellar motor to maximize the bacterial swimming speed for a given load. This condition is independent of the geometric optimality condition derived by Purcell and interestingly this condition is not satisfied by wild-type E. coli which swim 2-3 times slower than the maximum possible speed given the amount of available motor torque. Our analysis also reveals the existence of an anomalous propulsion regime, where the swim speed increases with increasing load (drag). Finally, we present experimental data which supports our analysis

A Null-model Exhibiting Synchronized Dynamics in Uncoupled Oscillators

The phenomenon of phase synchronization of oscillatory systems arising out of feedback coupling is ubiquitous across physics and biology. In noisy, complex systems, one generally observes transient epochs of synchronization followed by non-synchronous dynamics. How does one guarantee that the observed transient epochs of synchronization are arising from an underlying feedback mechanism and not from some peculiar statistical properties of the system? This question is particularly important for complex biological systems where the search for a non-existent feedback mechanism may turn out be an enormous waste of resources. In this article, we propose a null model for synchronization motivated by expectations on the dynamical behaviour of biological systems to provide a quantitative measure of the confidence with which one can infer the existence of a feedback mechanism based on observation of transient synchronized behaviour. We demonstrate the application of our null model to the phenomenon of gait synchronization in free-swimming nematodes, C. elegans